Pathology foundation models for training-free case retrieval in salivary gland tumors

Maximilian J. Roesel, Niklas Kiermeyer, Philipp Keyl, Frederick Klauschen

In pathology, pattern recognition relies on a frame of reference built through extensive training and experience, which may still fall short when encountering rare cancer subtypes. Archives of previously diagnosed tumors often contain relevant precedents, yet identifying the most relevant cases remains challenging. Here we explore whether content-based retrieval with current pathology foundation models facilitates rare cancer diagnostics without any task-specific training. Pathologists can query a digitized archive using a region of interest (ROI) from a whole slide image (WSI) and retrieve morphologically similar cases, along with their ICD-O codes and corresponding WSIs. The ROI can be selected manually or automatically using a gated attention-based multiple instance learning model. We evaluate our approach by leave-one-case-out on an imbalanced dataset of 137 salivary gland tumor cases spanning 12 ICD-O morphology categories, comparing four pathology foundation models (Atlas2, Atlas2-B, Atlas2-S, and UNI2h). Top-1/3/5 retrieval was 62.5%/76.7%/81.3% for Atlas2, 50.2/66.6/72.9% for UNI2h, 52.3%/71.5%/77.6% for Atlas2-B and 54.4/65.2/73.7% for Atlas2-S. Macro-averaged F1 ranged…